Scientific Software

October 18th, 2010

Two fairly interesting articles about scientific software appeared in Nature News this week. The first is an exhortation to scientists that can be summed up as: “Your code is good enough – publish it already!” (sounds familiar)

The second is a nice piece by Zeeya Merali warning about the dangers that lurk in scientific programs. The article gives a few examples of papers that had to be retracted because of buggy software, and then does a decent job of summing up many of the problems: untested code, poor documentation, and journals that don’t require code release along with publications.

While she talks about some potential solutions, including openness, better training, and collaborations with trained computer scientists, I feel like she glosses over a crucial point: The reason that we don’t have better scientific software is because it isn’t well-incentivized by the scientific community.

Grants are awarded for work on sexy diseases, not for reliable and robust software engineering. Don’t get me wrong – efforts like BioPerl and Bioconductor are fantastic community resources, but I’d argue that they’re examples of how good things can be despite a lack of systematic support. Allocating serious funding to groups that can produce platforms of solid, well-tested bioinformatics code would go a long way towards helping data science keep pace with the deluge of biological data that’s surging towards us.


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One Response to “Scientific Software”

  1. Hi Chris,
    nice post! I totally agree with you:
    – publish early vs. lack of testing/documentation.
    – bias of funds towards “sexy” projects.

    What can be done about it?

    Cheers,
    Claus